Free Your Mind
by T. E. Rankin
Summary: this is a story where the various fictional worlds are just diffrent servers on The Matrix, and Naruto, Akatsuki and the other containers have been freed. NarutoXfemKyuubi


AN: I know I said I was going to be at boot camp but right after my last update my ship date was moved. Well this is my next story, the other ones (and this one) will update sporadically. I want this story to be mostly Naruto and matrix, but there will be a lot of others mixed in really I can have just about any story in it the way I'm working it, so if you have any suggestions please make them in your review.

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Naruto had finally gotten Sasuke to come back to Konoha, just to be betrayed by his brother and was now floating in the air supported by youkai. It was painful, very painful; it felt like his soul was being sucked from his body. The pain was so immense that he passed out.

When Naruto came to he was in a pod with various wires attached and a tube going down his throat, after he pulled it out he became vaguely aware that a woman was in a tube next to him, in a similar predicament. A robot came from nowhere and attached to his head and unscrewed the wire that was attached to the back of his head. Then with a great rushing sound he was sent out of the pod and into a flume like tunnel system he was vaguely aware that the woman that was in the pod next to his was only slightly further behind him. Naruto was suddenly aware that the ride had ended and that he was in for a fall. Using his shinobi training, he quickly righted himself and was able to catch the woman. He was able to stand on the surface of the water just long enough to catch the woman before his strength went out and he fell into the lake taking the woman with him.

Minato was pacing back and forth in the hatch room waiting for his son to land in the flush lake. A light turned on and he opened the hatch and let the claw drop so Naruto could be lifted into the hovercraft.

Naruto saw a circle of light hovering above them, him and the woman, and what looked like a claw lowering to their position. Being very tired and not fully being able to move correctly, Naruto was unable to fight against being grabbed, and with the woman, was brought them onboard.

Minato looked at the people that he had just brought up to the ship. He was highly surprised that the woman was with Naruto, there had never been two people freed at the same time before, even when they had tried it. He chuckled and thought, "Looks like what Itachi said about his title as 'number one most surprising ninja' was right."

Naruto looked up and saw Minato and thought, "Great, I actually am dead," then passed out.

Minato sighed and picked up the two young adults and wrapped them in separate blankets, then brought them to a spare room, until they regained consciousness. After he had placed them on cots Minato went to report in.

Madara was waiting for Minato to report about Naruto's condition, when he heard a knock at the door. He shouted, "Come in."

Minato walked in and said, "Madara there is some surprising news. There was a young woman freed with Naruto. I'm not sure who it is either, perhaps you know."

Madara nodded and said, "Lead me to her, I'll get Itachi, he's been studying Naruto's patterns the most so he should know her."

"I don't know who she is." Itachi said as he looked at the unconscious red-head that was with Naruto. The young woman's eyes fluttered open as she took in her surroundings. Her face went through a myriad of emotions, stating with surprise and ending with concern.

The woman asked, "Where am I, the last thing I remember is being extracted."

This statement surprised everyone, and with a guard up Madara asked, "Who are you, when you answer we'll answer your questions?"

The woman said, "I am Kyuubi no Yoko, and I was sealed inside Naruto-kun."

Everyone took a step back and Itachi said, "You can't be Kyuubi, we deleted him, and Kyuubi was an AI so he couldn't have had a body."

Kyuubi looked offended and replied, "First, I'm female, I can't exactly have a high voice when a human could walk through my voice-box, and second, I preferred to be called a construct, AI implies that I'm not actually intelligent, when only Nara's and a couple Uchiha's are possibly more intelligent than me. As to why I have a body, I have no idea, but I can tell you that my body is an organic gynoid so I'm almost as human as you are. And before you kill me, realize that I am no long connected with the machines and I am more loyal to Naruto than them, at least he had some concern for me. He was more careful when he found out that I would die if he died, although I don't think he realized it."

Everyone else said, "Wow," at her story. Minato the said, "If you are Kyuubi then I just want to make sure that you wont do anything against us, so I'm going to put a power suppression seal on you to make it where Sarutobi, Madara, or I could stop you if it comes to that, because it sounds like you are your own person and you might be able to give us an edge above the machines."

Kyuubi agreed quickly, not seeing any way around it and left with Minato and Madara to get the seal, and Itachi left to get Sarutobi to watch over Naruto because it would not do for him to fly into a rage and kill everyone thinking they were enemies.

Naruto slowly awoke and saw another person he though dead, Sarutobi, watching over him. He said, "So I really am dead, great."

Sarutobi smiled and said, "Naruto, you are not dead and neither am I, we are merely free of the prison known as the Matrix."

Naruto asked, "What's the Matrix, and how did we get free of it?"

Sarutobi replied, "The Matrix is basically a machine generated genjutsu, one that cannot be escaped by conventional means. The only way is for someone who has already been released help you escape.

Now, I'm going to bring you out to the mess-hall for some food, but you must remember that anyone you see are allies, this means the entirety of the Akatsuki are not foes, they are the ones that released you, and me, though I imagine that my way hurt a lot less."

Naruto then asked, "What about the Kyuubi, I thought they were trying to extract her from me."

Sarutobi said, "Yes, they were and succeeded in extracting her, as they were for all the jinchuuriki, but the biju, after the powers were copied into the host, were deleted, so the biju ceased to exist." Then noticing the sudden depression that Naruto was in he quickly amended, "But Kyuubi was an anomaly, she was actually released with you that's who the woman that you caught was. It's very surprising, now come on and you can go meet up with her, and some of the other ex-jinchuuriki that we have onboard.

When they went into the mess hall there were four people sitting around. Sarutobi pointed to each of them and said, "Itachi, Sasuke and Gaara, you already know." Then he pointed at the orange haired person and said, "This is Pein, the figure-head of the Akatsuki."

Naruto was surprised that Itachi and Sasuke were being civil towards each other and voiced hi opinion.

Itachi replied, "I told Sasuke what actually happened when I fled the village."

Flashback

Itachi had just been approached by Pein who explained the matrix to him; he was pondering it and had gone to his best friend, Shisui, for help making this decision, after he had told Shisui about the proposition he had morphed into what looked like an ANBU with a blank mask. The ANBU would dodge everything that Itachi threw at it, but eventually Itachi was able to trick it with a genjutsu and killed it. When it was dead the ANBU morphed back into Shisui and Itachi realized that he had gotten the Mangekyou.

As he went back home to tell his father what had happened the ANBU-like people came out and he was unable to defeat them. Cornered and about to be killed by the ANBU, Itachi was saying his prayers when a black fireball consumed the ANBU and Madara jumped down and helped Itachi to his feet and asked, "Do you believe me now?" Itachi nodded and Madara continued, "I can sense more agents coming you should go make sure that anything that you need done is done."

Itachi replied, "I just want to get a letter to give my girlfriend before we go, I'll meet you at the north gate in ten minutes."

Madara was dealing with the many agents that were coming out of the wood-work as Itachi ran into his home and grabbed a letter, as he was leaving he was ambushed by two agents, as Madara called them, he was able to overpower and kill one of them, who turned into his father. He realized who the other must be, and knowing that he couldn't kill his mother, no matter the reason, he used all of his skill to knock out the other agent, and when the agent became unconscious it turned back into Mikoto. Right after they changed back into who they actually were Sasuke came into the room. Itachi's eyes widened and thought, "No, I can't let them get Sasuke." He used Tsukuyomi on Sasuke so his mind would break slightly and give him a strong enough emotion to keep his mind from being taken over, unfortunately hate was the only one he could give him fast enough to keep him from turning. Quickly running out of the clan compound, while carrying his mother to free her as well, Itachi ran east towards his girlfriend's home to leave the message for her. Realizing he didn't have enough time to break into her room to leave it he just left it on the counter of the restaurant that was under her home that she worked at; then left to meet with Madara to escape the matrix.

Just before he got out of ear shout he heard a loud voice proclaim, "Ayame, there's a letter here for you."

/flashback

Naruto said, "So, your mother is still alive?"

Sasuke said, "Yes, and that is most of the reason that I forgave Itachi, when I met her it was proof of his story."

Naruto asked, "Where is she?"

Itachi replied, "She's at Zion, which is where we are going to go to restock, then we'll make a move to free our server now that we have all nine biju, then well go to the server 0100100001010000, some of the people in it can give off EMPs at will."

Pein put in, "The way that we are going to free everyone is essentially by destroying the virtual world so that everyone has to be unplugged. Which is why we needed to get rid of the biju, they regulated our server and now that they don't exist we can blow the crap out of it, which will cause the system to crash and there by release everyone."

The trip from the flush lake to Zion was, fortunately, an uneventful one. The ship had just docked and the crew was unloading as the one next to them was loading. Madara noticed the captain and shouted, "Hey, Morpheus, we finally got all the regulators out of your server."

Morpheus changed direction and walked up to them and smiled, "That's great, looks like we'll be one step closer to freeing man kind, when are you going to set up that "Hidden village" on the surface?"

Madara replied, "After we free server 0100100001010000, they'll be able to get a sustainable barrier up, we'll start working on getting the surface ready on our next mission.

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A.N. - I have been working on this for a while, and rewrote most of it a couple times. I'll be updating in a while. I hope you like it and the next server is another crossover the name is binary, and a cookie to anyone who figures out the next crossover. Ja Ne.


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